JAL-2388 Working hidden regions hide/show in desktop

[jalview.git] / src / jalview / io / JSONFile.java

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 36980f8..8dbede6 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -32,7 +32,7 @@ import jalview.bin.BuildDetails;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -46,8 +46,10 @@ import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
 import jalview.json.binding.biojson.v1.SequencePojo;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.ColorUtils;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
 import java.awt.Color;
@@ -71,10 +73,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private String application = "Jalview";
 
-  public static final String FILE_EXT = "json";
-
-  public static final String FILE_DESC = "JSON";
-
   private String globalColourScheme;
 
   private boolean showSeqFeatures;
@@ -85,9 +83,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private FeatureRenderer fr;
 
-  private List<int[]> hiddenColumns;
-
-  private ColumnSelection columnSelection;
+  private HiddenColumns hiddenColumns;
 
   private List<String> hiddenSeqRefs;
 
@@ -105,9 +101,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     super(source);
   }
 
-  public JSONFile(String inFile, String type) throws IOException
+  public JSONFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   @Override
@@ -118,7 +115,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   }
 
   @Override
-  public String print()
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     String jsonOutput = null;
     try
@@ -171,7 +168,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       }
 
       int count = 0;
-      for (SequenceI seq : seqs)
+      for (SequenceI seq : sqs)
       {
         StringBuilder name = new StringBuilder();
         name.append(seq.getName()).append("/").append(seq.getStart())
@@ -218,17 +215,20 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       {
         // These color schemes require annotation, disable them if annotations
         // are not exported
-        if (globalColourScheme.equalsIgnoreCase("RNA Helices")
-                || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
+        if (globalColourScheme
+                .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
+                || globalColourScheme
+                        .equalsIgnoreCase(JalviewColourScheme.TCoffee
+                                .toString()))
         {
-          jsonAlignmentPojo.setGlobalColorScheme("None");
+          jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
         }
       }
 
       if (exportSettings.isExportFeatures())
       {
         jsonAlignmentPojo
-                .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
+                .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
       }
 
       if (exportSettings.isExportGroups() && seqGroups != null
@@ -238,8 +238,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         {
           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
           seqGrpPojo.setGroupName(seqGrp.getName());
-          seqGrpPojo.setColourScheme(ColourSchemeProperty
-                  .getColourName(seqGrp.cs));
+          seqGrpPojo.setColourScheme(seqGrp.getColourScheme()
+                  .getSchemeName());
           seqGrpPojo.setColourText(seqGrp.getColourText());
           seqGrpPojo.setDescription(seqGrp.getDescription());
           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
@@ -278,8 +278,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     // hidden column business
     if (getViewport().hasHiddenColumns())
     {
-      List<int[]> hiddenCols = getViewport().getColumnSelection()
-              .getHiddenColumns();
+      List<int[]> hiddenCols = getViewport().getAlignment()
+              .getHiddenColumns()
+              .getHiddenRegions();
       StringBuilder hiddenColsBuilder = new StringBuilder();
       for (int[] range : hiddenCols)
       {
@@ -318,11 +319,18 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   }
 
   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
-          List<SequenceI> seqs, FeatureRenderer fr)
+          SequenceI[] sqs, FeatureRenderer fr)
   {
     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
-    for (SequenceI seq : seqs)
+    if (sqs == null)
+    {
+      return sequenceFeaturesPojo;
+    }
+
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+
+    for (SequenceI seq : sqs)
     {
       SequenceI dataSetSequence = seq.getDatasetSequence();
       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
@@ -344,7 +352,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                   String.valueOf(seq.hashCode()));
 
           String featureColour = (fr == null) ? null : jalview.util.Format
-                  .getHexString(fr.findFeatureColour(Color.white, seq,
+                  .getHexString(finder.findFeatureColour(Color.white, seq,
                           seq.findIndex(sf.getBegin())));
           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
@@ -522,8 +530,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         }
         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
                 displayBoxes, displayText, colourText, startRes, endRes);
-        seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
-                seqGrp);
+        seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
+                colourScheme, seqGrp));
         seqGrp.setShowNonconserved(showNonconserved);
         seqGrp.setDescription(description);
         this.seqGroups.add(seqGrp);
@@ -561,7 +569,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
             annotations[count] = new Annotation(displayChar, desc, ss, val);
             if (annot.get("colour") != null)
             {
-              Color color = UserColourScheme.getColourFromString(annot.get(
+              Color color = ColorUtils.parseColourString(annot.get(
                       "colour").toString());
               annotations[count].colour = color;
             }
@@ -657,12 +665,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
     if (hiddenCols != null && !hiddenCols.isEmpty())
     {
-      columnSelection = new ColumnSelection();
+      hiddenColumns = new HiddenColumns();
       String[] rangeStrings = hiddenCols.split(";");
       for (String rangeString : rangeStrings)
       {
         String[] range = rangeString.split("-");
-        columnSelection.hideColumns(Integer.valueOf(range[0]),
+        hiddenColumns.hideColumns(Integer.valueOf(range[0]),
                 Integer.valueOf(range[1]));
       }
     }
@@ -735,6 +743,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   @Override
   public void configureForView(AlignmentViewPanel avpanel)
   {
+    if (avpanel == null)
+    {
+      return;
+    }
     super.configureForView(avpanel);
     AlignViewportI viewport = avpanel.getAlignViewport();
     AlignmentI alignment = viewport.getAlignment();
@@ -744,15 +756,17 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     fr = avpanel.cloneFeatureRenderer();
 
     // Add non auto calculated annotation to AlignFile
-    for (AlignmentAnnotation annot : annots)
+    if (annots != null)
     {
-      if (annot != null && !annot.autoCalculated)
+      for (AlignmentAnnotation annot : annots)
       {
-        annotations.add(annot);
+        if (annot != null && !annot.autoCalculated)
+        {
+          annotations.add(annot);
+        }
       }
     }
-    globalColourScheme = ColourSchemeProperty.getColourName(viewport
-            .getGlobalColourScheme());
+    globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
     setDisplayedFeatures(viewport.getFeaturesDisplayed());
     showSeqFeatures = viewport.isShowSequenceFeatures();
 
@@ -774,20 +788,15 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return annotations;
   }
 
-  public List<int[]> getHiddenColumns()
-  {
-    return hiddenColumns;
-  }
-
   @Override
-  public ColumnSelection getColumnSelection()
+  public HiddenColumns getHiddenColumns()
   {
-    return columnSelection;
+    return hiddenColumns;
   }
 
-  public void setColumnSelection(ColumnSelection columnSelection)
+  public void setHiddenColumns(HiddenColumns hidden)
   {
-    this.columnSelection = columnSelection;
+    this.hiddenColumns = hidden;
   }
 
   @Override